The goal of {ensemblr} is to provide an R client to the Ensembl REST
API.
Please note that this package is still in its infancy and hence only a
small fraction of the resources exposed by the Ensembl REST API are
retrievable via {ensemblr}. You can check the functionality covered so
far in Ensembl REST API
Coverage.
You can install the current, very experimental version of
{ensemblr} with:
# install.packages("pak")
pak::pak("patterninstitute/ensemblr")TODO
Retrieve human linkage disequilibrium information for variants within a
1 kilobase window centred on variant 'rs123':
library(ensemblr)
get_ld_variants_by_window("rs123", genomic_window_size = 1L)
#> # A tibble: 6 × 6
#> species_name population variant_id1 variant_id2 r_squared d_prime
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs124 0.722 1.00
#> 2 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs122 0.722 1.00
#> 3 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs115 0.721 1.00
#> 4 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs12536724 0.255 1.00
#> 5 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs10239961 0.255 1.00
#> 6 homo_sapiens 1000GENOMES:phase_3:CEU rs123 rs114 0.475 0.703Please note that the {ensemblr} project is released with a
Contributor Code of Conduct. By
contributing to this project, you agree to abide by its terms.
The {ensemblr} logo, ensemblr.png, is a derivative work of an
illustration of “The small DNA double helix in PDB entry
309d”
by David S. Goodsell and the RCSB
PDB, used under
CC-BY-4.0.
ensemblr.png is licensed under CC-BY-4.0 by Ramiro Magno.
- R package rensembl by David Winter: https://github.com/dwinter/rensembl
- Python package ensembl-rest by Andrés García: https://github.com/Ad115/EnsemblRest
- Python package ensembl by Katsuya Noguchi: https://github.com/kn/ensembl